Biofuel researchers have developed a mechanism that may increase yields for products like diesel, ethanol and even medicines.

Growing bacteria, algae and plants on large scales is challenging enough; getting them to do things they don't normally do, like make fuel, is even harder.

Scientists have to select and tweak molecular pathways to make cells produce enough useful products to be economically viable. But these modified pathways are fragile, vulnerable to changes in the organism's environment. These products and their precursors can also be toxic to the cells that produce them.

Take yeast, for instance. The fungus ferments sugar into ethanol, the process used to make wine and beer. However, ethanol, an alcohol, poisons yeast, and even specially bred strains will only tolerate upward of 20 percent alcohol in their environment before they die off.

To make a stronger drink, you have to distill the liquid, which is a very energy-intensive process since it involves boiling and condensing the product.

Engines require a very pure energy source, so a 20 percent fuel concentration just won't do. However, purifying biological products to usable levels raises production costs beyond what most people will pay for, but with a new molecular control system, researchers expect to engineer more robust microbes and increase biofuel yields, making living organisms a more viable energy source.

Keeping cells from poisoning themselves
Scientists at the Joint BioEnergy Institute (JBEI) in California developed a dynamic sensor-regulator system (DSRS). It acts as a shock absorber, slowing down chemical production in a cell before it reaches toxic levels and scaling it back up when the coast is clear. Organisms using a DSRS survive longer and produce more fuel. The team published their findings last month in Nature Biotechnology.

In this case, researchers used a version of the bacterium Escherichia coli engineered to produce diesel fuel. Fuzhong Zhang, a postdoctoral researcher in the Keasling Laboratory at JBEI and the report's lead author, explained that in previous experiments, biofuel production fell short of its full potential.

"There are lots of factors you have to balance very well to get even close to the theoretical limit," he said.

Though the diesel product itself is not very dangerous to E. coli, several of its precursors, like fatty acids and ethanol, can harm the cell in high concentrations. The challenge is, then, to produce enough fuel without letting the intermediates build up.

Because they are living organisms, the cells also cannot neglect their basic functions like harvesting energy, excreting waste and making copies of themselves. As a result, simply cranking biofuel production up to 10 would not be effective. This is where the DSRS comes in.

"Nature has evolved a bunch of naturally occurring sensors for us," said Zhang. "In our case, we used a completely synthetic approach that we engineered from basic biological elements."

The researchers used a molecule that responds to high precursor concentrations, triggering cells to produce enzymes that convert the intermediate molecules into the final diesel product before they became toxic. Bacteria engineered with a DSRS produced up to three times more fuel than those without.

A refinery run by bacteria
James Carothers, a research scientist at JBEI and the University of California, Berkeley, who also co-authored the paper, said these results are generalizable and can be used in other pathways, not just to make fuel, but to make drugs like insulin.

In addition, Carothers said having a dynamic sensor gives engineers some wiggle room when tweaking a cell. Thus, scientists do not have to precariously balance every process in an organism when engineering processes and can instead count on a DSRS to compensate for the ebb and flow of cellular conditions. This makes for more resilient microbes and opens the door to more experiments.

However, there are some obstacles in applying this approach to other mechanisms. "The biggest challenge to this system is that you first of all have to have a sensor available. There is not always a sensor available," Zhang said, explaining that a specific regulation mechanism might not exist in nature, so scientists would have to engineer an artificial one, which is no small task.

In the future, energy companies could simply skim biofuels from vats of bacteria engineered with DSRS without all of the processing currently needed. Carothers said the team will now work on improving the sensor's efficiency and try to implement it in pathways for other useful molecules.